Predicting the Onset of Nonlinear Pharmacokinetics

Size: px
Start display at page:

Download "Predicting the Onset of Nonlinear Pharmacokinetics"

Transcription

1 Citation: CPT Pharmacometrics Syst Pharmacol (208) 7, ; doi:0002/psp4236 ARTICLE Predicting the Onset of Nonlinear Pharmacokinetics Andrew M Stein and Lambertus A Peletier 2 When analyzing the pharmacokinetics (PK) of drugs, one is often faced with concentration C vs time curves, which display a sharp transition at a critical concentration For C >, the curve displays linear clearance and for C < clearance increases in a nonlinear manner as C decreases Often, it is important to choose a high enough dose such that PK remains linear in order to help ensure that continuous target engagement is achieved throughout the duration of therapy In this article, we derive a simple expression for for models involving linear and nonlinear (saturable) clearance, such as Michaelis- Menten and target- mediated drug disposition (TMDD) models CPT Pharmacometrics Syst Pharmacol (208) 7, ; doi:0002/psp4236; published online on 08 September 208 Study Highlights WHAT IS THE CURRENT KNOWLEDGE ON THE TOPIC? Mathematical models of nonlinear PK and TMDD of mabs are widely used to guide drug development Often, it is important to choose a high enough dose such that PK remains linear to help ensure that continual target engagement is achieved throughout the duration of therapy There has not yet been a demonstration for how the PK/ pharmacodynamic parameters impact the onset concentration at which the nonlinearity is observed WHAT QUESTION DID THIS STUDY ADDRESS? How the PK and binding properties of the drug impact the onset of nonlinear PK WHAT DOES THIS STUDY ADD TO OUR KNOWLEDGE? was derived and was found to be equal to /Cl for the Michaelis- Menten model or k syn /(Cl/V c ) for the TMDD model HOW MIGHT THIS CHANGE DRUG DISCOVERY, DEVELOPMENT, AND/OR THERAPEUTICS? The parameter can be used to provide better intuition for how the PK parameters impact drug concentration profiles and, in particular, guide the modeler in understanding where the random effects may need to be added and what parameters of the model are identifiable When analyzing the pharmacokinetics (PK) of drugs, one is often faced with concentration vs time curves which display a sudden increase in the elimination rate below a certain critical concentration ( ) Examples of this phenomenon, in which the PK exhibit this nonlinear behavior, are shown in Figure for efalizumab (anti- CDa), mavrilimumab (antigranulocyte- macrophage colony- stimulating factor receptor), 2 and romosozumab (antisclerostin) 3 This nonlinearity shown in Figure results from a combination of two pathways of drug clearance: (i) a linear, nonspecific clearance due to endocytosis; and (ii) a nonlinear, saturable clearance due to internalization of the target receptor: At high drug concentrations, the target receptor is saturated and the rate of elimination is governed by the nonspecific clearance At lower drug concentrations, when the target receptor is no longer saturated, both the nonspecific route and the saturable route contribute to drug clearance and, hence, the rate of elimination increases as the concentration decreases A common goal when selecting the dose and regimen of a drug is to maintain a drug concentration that stays above the There are two reasons for this goal Ensure lower PK variability in the population, because may vary between subjects 2 Ensure that target occupancy remains high, as maintaining drug concentrations above is thought to be a necessary (although not sufficient) condition to maintain target saturation 4 In this article, we show examples of systems that have a simple critical value for the drug concentration such that as long as the drug concentration remains above this value, target mediated elimination is saturated and the PK is linear In Figure, is illustrated; when the concentration falls below, the elimination rate suddenly increases Novartis Institute for BioMedical Research, Cambridge, MA, USA; 2 Mathematical Institute, Leiden University, RA, Leiden, The Netherlands *Correspondence: Andrew M Stein (andrewstein@novartiscom) Received 2 February 208; accepted 27 April 208; published online on 08 September 208 doi:0002/psp4236

2 67 Figure Nonlinear pharmacokinetics for efalizumab, mavrilumab, and romosozumab Note that for all three drugs, as the concentration drops below the critical concentration ( ), the elimination rate suddenly increases We derive an analytical expression for for both the Michaelis-Menten model,5 and the target- mediated drug disposition model (TMDD) 6 8 Both models have two routes of clearance: nonspecific- linear elimination and saturablenonlinear elimination Both analyses will be discussed in the absence and in the presence of a peripheral compartment In the presence of a peripheral compartment, the analysis becomes more complex, but it is still transparent in common cases, such as rapid exchange between the two compartments In all cases, is independent of drug dose and volume of distribution (a) (b) METHODS For modeling the onset of the PK nonlinearity, we focus on the two models that are frequently used by the pharmacometrics community: Michaelis- Menten and TMDD A more general theoretical derivation of for any PK model is beyond the scope of this article We start by focusing on the simpler case of the one- compartment model and then extend this analysis to the twocompartment scenario The two- compartment models are shown schematically in Figure 2 below The corresponding one- compartment models are identical with the models shown in Figure 2, except that the peripheral compartments (C p ) are removed Michaelis- Menten elimination One- compartment model The basic model for linear and nonlinear drug elimination involves a single (central) compartment and a single differential equation for the concentration C of the drug involving linear and saturable elimination side by side: V c = Cl C V C max C+K M Here, V c is the volume of the central compartment, Cl a first order clearance rate, is the maximum rate of () Figure 2 Structural scheme of the basic model describing (a) Michaelis- Menten kinetics and (b) target- mediated drug disposition (TMDD) where a drug C binds a target receptor R which is synthesized by a zero order reaction and degenerates according to a first order reaction Drug and target form a complex CR, which internalizes through a firstorder reaction saturable elimination and K M is the Michaelis- Menten constant For an initial iv bolus dose D, the initial concentration is given by C(0) = D/V C Two- compartment model When the drug is distributed over a central compartment with concentration C c and a peripheral compartment C p, with linear and nonlinear elimination occurring only from the central compartment, the PK are described by the system of equations: V c c V p p = Cl C c Q(C C c +K c C p ) M in which exchange between the compartments is driven by the difference in drug concentration in the two compartments (ie, by the term Q(C c C p ) where Q denotes a nonspecific clearance rate) C c = +Q(C c C p ) (2) wwwpsp-journalcom

3 672 Table Parameters for mavrilimumab, efalizumab, and romosozumab, based on fits to data Mavrilimumab Efalizumab Romosozumab Units Weight- based dose mg/kg Equivalent molar dose nmol V c L V p L Cl L/d Q L/d k syn = /V c nm/d K ss = K M 2 2 nm k e(r) /d k e(cr) /d k off 0 /d k on = (k off + k e(cr) )/K ss /(nm d) Cl, clearance; k e(c), drug elimination rate; k e(r), receptor elimination rate; K M, Michaelis-Menten constant; k off, dissociation rate; k on, association rate; Kss, quasi-steady-state constant; k syn, receptor synthesis rate; Q, intercompartmental clearance; V c, central volume;, maximal rate of saturable (nonlinear) elimination; V p, peripheral volume If initially, an iv bolus dose D is supplied to the central compartment while the peripheral compartment is empty, the initial conditions are here C c (0) = D/V c and C p (0) = 0 Target- mediated drug disposition In its most elementary form, TMDD target kinetics is assumed to follow a zero- order production rate k syn and a firstorder elimination rate k e(r) R The formation of drug- target complex CR takes place via a second- order process k on C R, a first- order loss of the drug- receptor complex via k off CR, and an irreversible first- order elimination process k e(cr) CR In Figure 2 this system of reactions is shown schematically One- compartment model Mathematically, the onecompartment TMDD model is described by the system of differential equations below: = k onc R+k off CR k e(c) C; k e(c) = Cl v C dr = k syn k on C R+k off CR k e(r) R R = k on C R k off CR k e(cr) CR Note that in the absence of drug, the steady- state target concentration is given by R 0 = k syn /k e(r) Here, we assume that the drug is supplied through an iv bolus dose D to the system when it is free from drug and the target is at steady state (ie, C(0) = D/V c, R(0) = R 0 and CR(0) = 0) By adding the first and the third equations, we obtain an equation for the total amount of drug C tot = C + CR and, similarly, by adding the second and the third equations we obtain an equation for the total amount of the target, R tot = R + CR: tot = k e(c) C k e(cr) CR dr tot = k syn k e(r) R k e(cr) CR Note that the on- rate and the off- rate constants k on and k off no longer appear in these equations (3) (4) In practice, drug binding and complex internalization is fast, so that after a short time drug, target, and drug- target complex are in quasi- steady- state (QSS) 9 (ie, C, R, and CR) are approximately related through the expressions: where K SS C CR = R tot and R = R C+K tot SS C+K SS K SS = k off +k e(cr) k on Two- compartment model The two- compartment model is similar to the one- compartment model with the addition of a peripheral compartment with the initial condition C p (0) = 0 tot ptot = k e(c) C k e(cr) CR Q(C C p ) = +Q(C C p ) dr tot = k syn k e(r) R k e(cr) CR Model analysis, fitting, and simulation A mathematical analysis of the above equations was performed to derive for each model above To test the theory, the data from Figure was fit to the twocompartment TMDD model from Eq 7 where it was assumed that k e(r) = k e(cr) This assumption is typically made when fitting the PK for membrane- bound targets where it can be especially difficult to estimate k e(r) 0 Good fits can still be achieved even when implementing this constraint Sensitivity analyses were performed for the onecompartment Michaelis- Menten and TMDD models and the (5) (6) (7) CPT: Pharmacometrics & Systems Pharmacology

4 673 Concentration (nm), , dose (mg/kg) 00 Vc (L) Vmax (nmol/day) Km (nm) Month CL (L/day) fold change in parameter 0x 3x x 03x 0x Figure 3 Mavrilimumab: one- compartment model in Eq in which the base parameter values are in Table Each plot shows a sensitivity analysis where the parameter in the title is changed from 0- fold to 0- fold The dot shows critical concentration CL, clearance;, maximal rate of saturable elimination two- compartment Michaelis- Menten model In the sensitivity analysis, one parameter at a time was changed while all other parameters were held fixed, and the calculated was plotted together with the simulated PK data Because dosing of monoclonal antibodies (mabs) is usually reported in mg/kg, but the binding model requires doses of nmol and concentrations of nm, a dose of 0 mg/kg is converted to nanomoles for the model simulations using the formula below, which assumes a 70 kg patient and a 50 kda drug (typical antibody) 0 mg kg 70 kg patient g 000 mg mol g 09 nmol = 467 nmol mol RESULTS Model fit The model fits to the data are shown in the Supplementary Material and the parameters from the fits that are subsequently used for simulations are listed in Table These parameters were also used to compute the lines, as described below Note that the large values for k e(r) and k e(cr) for romosozumab and efalizumab are due to the practical unidentifiability of these parameters Michaelis- Menten elimination One- compartment model For drug concentrations, which are either large or small with respect to K M, Eq can be approximated by the following simpler equations: V c = Cl C Cl C for C K M, ( ) V c = Cl + C for C K K M M Thus, on a logarithmic scale, the graph of C(t) will be approximately linear for both large and small values of C; for (8) the range of concentrations in between, the graph curves down connecting the upper linear segment with the lower linear segment (see Figure 3) Of particular interest is the situation when the rate of elimination increases substantially at low concentrations According to Eq 8, this is the case when: Cl K K M M Cl Throughout this article, it will be assumed that Eq 9 holds The sensitivity analysis for romosozumab in the Supplementary Material demonstrates that for small values of or large values of K M, the shoulder (where the onset of the PK nonlinearity is observed) disappears entirely and the PK appears linear As the concentration drops, the elimination rate increases, and it is important to know at which concentration this transition takes place We define this critical concentration,, as the value of C where the rate of elimination doubles from its value at large drug concentrations This definition was chosen because when the rate of elimination doubles, that means the linear and nonlinear components of elimination contribute equally is derived by dividing Eq by C, which gives: ( d V c log (C) = Cl + V ) max C+K M It can readily be seen that for large concentrations, the slope is Cl and, thus, the rate of elimination doubles when: = Cl or C = K () C+K M Cl M By assumption of Eq 9, we may neglect K M in the right expression in Eq and, thus, define the critical concentration to be: (9) (0) wwwpsp-journalcom

5 674 def = Cl (2) Note that neither the drug dose nor the volume V c of the central compartment enters the definition of In Figure 3, we show simulations of concentration graphs based on Eq for data from mavrilimumab in which Cl = 03 L/d, = 67 nmol/d, and K M = nm (Table ) Then, according to Eq 2, = 22 nm Note that here is large compared to K M so that for the base values condition Eq 9 is satisfied Figure 3 shows how, computed from Eq 2 and indicated by a dot, changes when one of the parameters involved in the model is varied In addition, it shows where fits in the concentration- time curve of the drug The graph for the largest parameter value is drawn in red and the graph for the smallest is drawn in magenta In the first panel in Figure 3, in which the dose is varied while keeping C(0) >, it is shown how both numerically and geometrically corresponds to the kink in the graph, irrespective of the dose value According to Eq 2, as increases, moves up, while as Cl increases moves down, and this is observed in the second and third panels Because does not depend on either V c or K M, it does not move in the fourth and the fifth panels Two- compartment model As we shall see, for initial drug concentrations that are large enough, the switch from linear to nonlinear drug elimination is apparent in this situation as well, and it is possible to identify a critical drug concentration Here, we only derive the formula for for the special case when drug exchange between the two compartments is fast relative to the nonspecific clearance (Cl) and the saturable clearance ( ), such as when: Q Cl and Q Under these conditions, it is found that the two concentrations, C c and C p, rapidly coalesce (ie, C c (t) C p (t) 0), and in both the central and peripheral compartments is given by the same formula as for the one- compartment model (ie, by Eq 2): = Cl (3) (4) The details of the derivation of Eq 4 are provided further below In Figure 4, we show simulations for the two- compartment Michaelis- Menten model for parameter values, which are varied around the base parameters listed in Table, as indicated in the headings of the different panels The graphs in the different panels are comparable to those shown in Figure 3 for the one- compartment model, except that many show a weak point of inflection below the Evidently, the location of on the graphs, as defined by Eq 4, has not changed much from what was seen in Figure 3 This is remarkable because the condition in Eq 3 is not satisfied by the base values of the parameters Specifically, the value of the intercompartmental clearance Q is not large compared to On the other hand, Q is indeed large compared to the nonspecific clearance Cl, as is also borne out by the different graphs shown in Figure 4, which exhibit a clear two- phase structure during the initial development Concentration (nm) 0,000, ,000, dose (mg/kg) 00 Vp (L) Vmax (nmol/day) Q (L/day) CL (L/day) Km (nm) Month Vc (L) fold change in parameter 0x 3x x 03x 0x Figure 4 Mavrilimumab two- compartment Michaelis- Menten model, in which the base parameter values are listed in Table, and each plot shows a sensitivity analysis in which the parameter in the title is changed from 0- fold to 0- fold The dot shows critical concentration CL, clearance;, maximal rate of metabolism CPT: Pharmacometrics & Systems Pharmacology

6 675 Rapid exchange between central and peripheral compartments Suppose that Q Cl and Q Then, when we divide the system of Eq 2 by Q, and scale the time variable according to τ = Qt, we obtain, with x (τ) = C c (τ/q) and y (τ) = C p (τ/q), where V dx c = ε x (x y) ν(τ), dτ dy V p dτ = x y ε = Cl Q and ν(τ) = C c Q C c +K M (5) (6) Adding the two equations we find for the total amount of drug: With these equalities, the system in Eq 4 can be approximated by the following pair of equations: Thus, when we subtract the second equation in Eq 23 from the first we obtain for 0 < t < t 0 or, when we multiply by V c, d (C+R tot) = k e(c) C k e(cr) R tot dr tot = k syn k e(cr) R tot = k e(c) C k syn V c = Cl C where = V c k syn (23) (24) (25) the conservation law: A(τ) def = V c x(τ)+v p x(τ), (7) This equation is formally the same as the first equation in the system of Eq 8 Following the reasoning used in the Michaelis- Menten elimination Subsection to derive, we assume, as in Eq 9, that: d dτ (V c x +V p y) = ε x ν 0 (8) Thus, there is very little loss of drug: on the fast time scale τ = O() (ie, t = O(/Q)) Similarly, by dividing the equations by their respective volumes and then subtracting the two equations we obtain: and show that Cl K ss or k syn k e(c) K ss (26) ( d (x y) + ) (x y) dτ V c V p so that C c (t) C p (t) 0 on the fast time scale as well Therefore, within a very short time, we may write A(t) = (V c + V p )C c (t) We now go back to Eq 8 and multiply it by Q so that the original time variable t is returned In light of Eq 9, this yields the following equation: V ss c = Cl C c C c +K M V ss = V c +V p where V ss is the volume of distribution at steady state Following the arguments given for the one- compartment model, we find that the formula for, as given by Eq 2, has not changed Target- mediated drug disposition (9) (20) One- compartment model Suppose that the drug concentration is large compared to the dissociation constant (ie, C(t) K SS over a period 0 < t < t 0 ) Then Eq 5 implies that during this interval we have: CR R tot and R 0 (22) C c (2) = Cl = k syn k e(c) (27) Thus, by assuming rapid drug binding and complex internalization, drug clearance can be seen as the sum of linear and Michaelis- Menten type elimination resulting in the same expression for the In Figure 5, we show simulations for the onecompartment Michaelis- Menten and TMDD models and we see that for mavrilimumab, a typical antibody for which Eq 26 is satisfied, simulations give corresponding results and, as we have seen in Figures 3 and 4 for the Michaelis- Menten model, fits snugly in the arm of the concentration curves In the first five graphs, in which simulations for the Michaelis- Menten model and the TMDD model are shown together (the Michaelis- Menten model is dashed and the TMDD is solid), the Michaelis- Menten model curves lie below the TMDD curves This can be understood by comparing the equations for C tot and R tot in Eqs 4 and 23 and remembering that CR < R tot The similarity between the Michaelis- Menten and TMDD models has been reported elsewhere 0, Comparable findings were observed for the two- compartment model as well Note that the similarity of the Michaelis- Menten and TMDD models may not apply for other biologics, such as bispecific wwwpsp-journalcom

7 676 Concentration (nm), , dose (mg/kg) 00 Kss (nm) 0 0 ksyn (nm/day) ker (/day) CL (L/day) kecr (/day) Vc (L) koff (/day) Month fold change in parameter 0x 3x x 03x 0x model TMDD MM Figure 5 Mavrilimumab one- compartment Michaelis- Menten model (MM; solid line) and target- mediated drug disposition (TMDD; dashed line) model, in which the base parameter values are in Table and each plot shows a sensitivity analysis where the parameters in the title is changed from 0- fold to 0- fold The dot shows critical concentration For the TMDD model, k syn = /V c, Kss = K M target engagers or cytokines where the doses are much lower 7,2 DISCUSSION In practice, is a useful quantity We list a few applications below One application of is in providing an initial estimate for or k syn from a graphical inspection of the data For large, iv doses, Cl can be estimated by noncompartmental analysis by computing the area under the curve (AUC) 0 for a single dose and then computing Cl = Dose/AUC 0- Then, can be estimated from a graph of the PK and Eq 4 is then applied to get = Cl or k syn = Cl/V c Another application is that when fitting a population PK model, there may be patients who have similar PK above (and, thus, similar Cl) but different levels When this is observed, we have found that a random effect on was needed to capture the intersubject variability in the low concentration data Finally, is also useful in understanding the identifiability of TMDD models when fit to data of the type shown in Figure Here, it has been shown that once the linear PK parameters have been identified (say from high- dose data) k syn is the only remaining parameter needed to determine Then, given k syn, K SS is the only remaining parameter needed to determine the slope of the nonlinearity Thus, these two parameters are often estimable from the nonlinear PK alone However, other parameters of the TMDD model, such as the receptor density R 0 = k syn /k e(r) (often assumed to be constant with k e(r) = k e(cr) ) is often not identifiable with PK data alone, as previously reported 0, One key assumption for the estimate to apply is that initially, the drug concentration is large so that the nonlinear elimination term initially has a negligible contribution to the PK curve If this assumption does not hold, there may be no kink and hence no In addition, there may be a kink, but if the dose is low enough such that the nonlinear component already contributes significantly to the elimination, as calculated here will not describe the kink In the extreme case that Cl 0 for a drug with only saturable elimination, and is essentially unobservable Thus as defined here is no longer of practical value in scenarios where the saturable route of elimination dominates for all observable drug concentrations, as is the case for drugs that are given at low doses, such as bispecific target engagers and cytokines To describe the kink in the PK curve in these scenarios (shown in more detail in the Supplementary Material) an alternative definition of would be needed is of its greatest utility for mabs (or other drugs) given at sufficiently high doses, such that both linear and nonlinear elimination phases are observable In summary, when developing antagonists, it is often the goal to pick a dosing regimen where the drug concentration stays above In this article, we have developed a simple formula for this critical concentration: = /Cl = k syn /k e(c) CPT: Pharmacometrics & Systems Pharmacology

8 677 Supplementary Information Supplementary informa tion accompanies this paper on the CPT: Pharmacometrics & Systems Pharmacology website(wwwpsp-journal com) Acknowledgment The authors would like to thank Johan Gabrielsson for many helpful discussions Source of Funding No funding was received for this work Conflict of Interest Andrew Stein is employed by Novartis Institute for BioMedical Research Author Contributions AMS and LAP wrote the manuscript AMS and LAP performed the research AMS and LAP analyzed the data Bauer, RJ, Dedrick, RL, White, ML, Murray, MJ & Garovoy, MR Population pharmacokinetics and pharmacodynamics of the anti- CDa antibody hu24 in human subjects with psoriasis J Pharmacokinet Biopharm 27, (999) 2 Burmester, GR, Feist, E, Sleeman, MA, Wang, B, White, B & Magrini, F Mavrilimumab, a human monoclonal antibody targeting GM- CSF receptor- α, in subjects with rheumatoid arthritis: a randomised, double- blind, placebo- controlled, phase I, first- in- human study Ann Rheum Dis 70, (20) 3 Padhi, D, Jang, G, Stouch, B, Fang, L & Posvar, E Single- dose, placebocontrolled, randomized study of AMG 785, a sclerostin monoclonal antibody J Bone Miner Res 26, 9 26 (20) 4 Cao, Y & Jusko, WJ Incorporating target- mediated drug disposition in a minimal physiologically- based pharmacokinetic model for monoclonal antibodies J Pharmacokinet Pharmacodyn 4, (204) 5 Michaelis, L & Menten, ML The kinetics of the inversion effect Biochem Z 49, (93) 6 Levy, G Pharmacologic target- mediated drug disposition Clin Pharmacol Ther 56, (994) 7 Mager, DE & Jusko, WJ General pharmacokinetic model for drugs exhibiting target- mediated drug disposition J Pharmacokinet Pharmacodyn 28, (200) 8 Mager, DE & Krzyzanski, W Quasi- equilibrium pharmacokinetic model for drugs exhibiting target- mediated drug disposition Pharm Res 22, (2005) 9 Peletier, LA & Gabrielsson, J Dynamics of target- mediated drug disposition: characteristic profiles and parameter identification J Pharmacokinet Pharmacodyn 39, (202) 0 Gibiansky, L, Gibiansky, E, Kakkar, T & Ma, P Approximations of the targetmediated drug disposition model and identifiability of model parameters J Pharmacokinet Pharmacodyn 35, (2008) Stein, AM Practical unidentifiability of receptor density in target mediated drug disposition models can lead to over-interpretation of drug concentration data biorxiv (207) 2 Klinger, M, et al Immunopharmacologic response of patients with B- lineage acute lymphoblastic leukemia to continuous infusion of T- cell engaging CD9/ CD3- bispecific BiTE antibody blinatumomab Blood 9, (202) 208 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc on behalf of the American Society for Clinical Pharmacology and Therapeutics This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes wwwpsp-journalcom

TMDD Model Translated from NONMEM (NM- TRAN) to Phoenix NLME (PML)

TMDD Model Translated from NONMEM (NM- TRAN) to Phoenix NLME (PML) TMDD Model Translated from NONMEM (NM- TRAN) to Phoenix NLME (PML) Phoenix Modeling Language School March 22, 2018 Loan Pham, Ph.D. Senior Pharmacokinetic Scientist Camargo Pharmaceutical Services 9825

More information

Noncompartmental vs. Compartmental Approaches to Pharmacokinetic Data Analysis Paolo Vicini, Ph.D. Pfizer Global Research and Development David M.

Noncompartmental vs. Compartmental Approaches to Pharmacokinetic Data Analysis Paolo Vicini, Ph.D. Pfizer Global Research and Development David M. Noncompartmental vs. Compartmental Approaches to Pharmacokinetic Data Analysis Paolo Vicini, Ph.D. Pfizer Global Research and Development David M. Foster., Ph.D. University of Washington October 28, 2010

More information

Noncompartmental vs. Compartmental Approaches to Pharmacokinetic Data Analysis Paolo Vicini, Ph.D. Pfizer Global Research and Development David M.

Noncompartmental vs. Compartmental Approaches to Pharmacokinetic Data Analysis Paolo Vicini, Ph.D. Pfizer Global Research and Development David M. Noncompartmental vs. Compartmental Approaches to Pharmacokinetic Data Analysis Paolo Vicini, Ph.D. Pfizer Global Research and Development David M. Foster., Ph.D. University of Washington October 18, 2012

More information

Nonlinear pharmacokinetics

Nonlinear pharmacokinetics 5 Nonlinear pharmacokinetics 5 Introduction 33 5 Capacity-limited metabolism 35 53 Estimation of Michaelis Menten parameters(v max andk m ) 37 55 Time to reach a given fraction of steady state 56 Example:

More information

The general concept of pharmacokinetics

The general concept of pharmacokinetics The general concept of pharmacokinetics Hartmut Derendorf, PhD University of Florida Pharmacokinetics the time course of drug and metabolite concentrations in the body Pharmacokinetics helps to optimize

More information

3 Results. Part I. 3.1 Base/primary model

3 Results. Part I. 3.1 Base/primary model 3 Results Part I 3.1 Base/primary model For the development of the base/primary population model the development dataset (for data details see Table 5 and sections 2.1 and 2.2), which included 1256 serum

More information

Multicompartment Pharmacokinetic Models. Objectives. Multicompartment Models. 26 July Chapter 30 1

Multicompartment Pharmacokinetic Models. Objectives. Multicompartment Models. 26 July Chapter 30 1 Multicompartment Pharmacokinetic Models Objectives To draw schemes and write differential equations for multicompartment models To recognize and use integrated equations to calculate dosage regimens To

More information

PHARMACOKINETIC DERIVATION OF RATES AND ORDERS OF REACTIONS IN MULTI- COMPARTMENT MODEL USING MATLAB

PHARMACOKINETIC DERIVATION OF RATES AND ORDERS OF REACTIONS IN MULTI- COMPARTMENT MODEL USING MATLAB IJPSR (2016), Vol. 7, Issue 11 (Research Article) Received on 29 May, 2016; received in revised form, 07 July, 2016; accepted, 27 July, 2016; published 01 November, 2016 PHARMACOKINETIC DERIVATION OF RATES

More information

Research Article. Michaelis-Menten from an In Vivo Perspective: Open Versus Closed Systems. Johan Gabrielsson 1 and Lambertus A.

Research Article. Michaelis-Menten from an In Vivo Perspective: Open Versus Closed Systems. Johan Gabrielsson 1 and Lambertus A. The AAPS Journal (201) 20: 102 DOI: 10.120/s1224-01-0256-z Research Article Michaelis-Menten from an In Vivo Perspective: Open Versus Closed Systems Johan Gabrielsson 1 and Lambertus A. Peletier 2,3 Received

More information

PHA 4123 First Exam Fall On my honor, I have neither given nor received unauthorized aid in doing this assignment.

PHA 4123 First Exam Fall On my honor, I have neither given nor received unauthorized aid in doing this assignment. PHA 4123 First Exam Fall 1998 On my honor, I have neither given nor received unauthorized aid in doing this assignment. TYPED KEY Name Question 1. / pts 2. /2 pts 3. / pts 4. / pts. / pts 6. /10 pts 7.

More information

Quantitative Pooling of Michaelis-Menten Equations in Models with Parallel Metabolite Formation Paths

Quantitative Pooling of Michaelis-Menten Equations in Models with Parallel Metabolite Formation Paths Journal of Pharmacokinetics and Biopharmaceutics, Vol. 2, No. 2, I974 Quantitative Pooling of Michaelis-Menten Equations in Models with Parallel Metabolite Formation Paths Allen J. Sedman ~ and John G.

More information

Impact of saturable distribution in compartmental PK models: dynamics and practical use

Impact of saturable distribution in compartmental PK models: dynamics and practical use J Pharmacokinet Pharmacon (2017) 44:1 16 DOI 10.1007/s1092-016-9500-2 ORIGINAL PAPER Impact of saturable distribution in compartmental PK models: namics and practical use Lambertus A. Peletier 1 Willem

More information

Beka 2 Cpt: Two Compartment Model - Loading Dose And Maintenance Infusion

Beka 2 Cpt: Two Compartment Model - Loading Dose And Maintenance Infusion MEDSCI 719 Pharmacometrics Beka 2 Cpt: Two Compartment Model - Loading Dose And Maintenance Infusion Objective 1. To observe the time course of drug concentration in the central and peripheral compartments

More information

Ordinary Differential Equations in Pharmacodynamics

Ordinary Differential Equations in Pharmacodynamics Ordinary Differential Equations in Pharmacodynamics L.A. Peletier Mathematical Institute, Leiden University PB 95, 3 RA Leiden, The Netherlands Tel: +3-7-54.6864, Fax: +3-7-54.979 e-mail: peletier@math.leidenuniv.nl

More information

On drug transport after intravenous administration

On drug transport after intravenous administration On drug transport after intravenous administration S.Piekarski (1), M.Rewekant (2) Institute of Fundamental Technological Research Polish Academy of Sciences (1), Medical University of Warsaw, Poland Abstract

More information

A nonlinear feedback model for tolerance and rebound

A nonlinear feedback model for tolerance and rebound A nonlinear feedback model for tolerance and rebound Johan Gabrielsson 1 and Lambertus A. Peletier 2 3 Abstract The objectives of the present analysis are to disect a class of turnover feedback models

More information

Enzyme Reactions. Lecture 13: Kinetics II Michaelis-Menten Kinetics. Margaret A. Daugherty Fall v = k 1 [A] E + S ES ES* EP E + P

Enzyme Reactions. Lecture 13: Kinetics II Michaelis-Menten Kinetics. Margaret A. Daugherty Fall v = k 1 [A] E + S ES ES* EP E + P Lecture 13: Kinetics II Michaelis-Menten Kinetics Margaret A. Daugherty Fall 2003 Enzyme Reactions E + S ES ES* EP E + P E = enzyme ES = enzyme-substrate complex ES* = enzyme/transition state complex EP

More information

Michaelis-Menten Kinetics. Lecture 13: Kinetics II. Enzyme Reactions. Margaret A. Daugherty. Fall Substrates bind to the enzyme s active site

Michaelis-Menten Kinetics. Lecture 13: Kinetics II. Enzyme Reactions. Margaret A. Daugherty. Fall Substrates bind to the enzyme s active site Lecture 13: Kinetics II Michaelis-Menten Kinetics Margaret A. Daugherty Fall 2003 Enzyme Reactions E + S ES ES* EP E + P E = enzyme ES = enzyme-substrate complex ES* = enzyme/transition state complex EP

More information

A Dynamical Systems Analysis of the Indirect Response Model with Special Emphasis on Time to Peak Response 1

A Dynamical Systems Analysis of the Indirect Response Model with Special Emphasis on Time to Peak Response 1 Journal of Pharmacokinetics and Pharmacodynamics, Vol.... A Dynamical Systems Analysis of the Indirect Response Model with Special Emphasis on Time to Peak Response 1 Lambertus A. Peletier 23, Johan Gabrielsson

More information

SIMPLE MODEL Direct Binding Analysis

SIMPLE MODEL Direct Binding Analysis Neurochemistry, 56:120:575 Dr. Patrick J. McIlroy Supplementary Notes SIMPLE MODEL Direct Binding Analysis The interaction of a (radio)ligand, L, with its receptor, R, to form a non-covalent complex, RL,

More information

MIDW 125 Math Review and Equation Sheet

MIDW 125 Math Review and Equation Sheet MIDW 125 Math Review and Equation Sheet 1. The Metric System Measures of weight are based on the gram (g): 1 kilogram = 1 kg = 1000 gram = 1000 g = 10 3 g 1 milligram = 1 mg = 10 3 g 1 microgram = 1 g

More information

Problem Set 2. 1 Competitive and uncompetitive inhibition (12 points) Systems Biology (7.32/7.81J/8.591J)

Problem Set 2. 1 Competitive and uncompetitive inhibition (12 points) Systems Biology (7.32/7.81J/8.591J) Problem Set 2 1 Competitive and uncompetitive inhibition (12 points) a. Reversible enzyme inhibitors can bind enzymes reversibly, and slowing down or halting enzymatic reactions. If an inhibitor occupies

More information

Confidence and Prediction Intervals for Pharmacometric Models

Confidence and Prediction Intervals for Pharmacometric Models Citation: CPT Pharmacometrics Syst. Pharmacol. (218) 7, 36 373; VC 218 ASCPT All rights reserved doi:1.12/psp4.12286 TUTORIAL Confidence and Prediction Intervals for Pharmacometric Models Anne K ummel

More information

F. Combes (1,2,3) S. Retout (2), N. Frey (2) and F. Mentré (1) PODE 2012

F. Combes (1,2,3) S. Retout (2), N. Frey (2) and F. Mentré (1) PODE 2012 Prediction of shrinkage of individual parameters using the Bayesian information matrix in nonlinear mixed-effect models with application in pharmacokinetics F. Combes (1,2,3) S. Retout (2), N. Frey (2)

More information

A Novel Screening Method Using Score Test for Efficient Covariate Selection in Population Pharmacokinetic Analysis

A Novel Screening Method Using Score Test for Efficient Covariate Selection in Population Pharmacokinetic Analysis A Novel Screening Method Using Score Test for Efficient Covariate Selection in Population Pharmacokinetic Analysis Yixuan Zou 1, Chee M. Ng 1 1 College of Pharmacy, University of Kentucky, Lexington, KY

More information

MITOCW enzyme_kinetics

MITOCW enzyme_kinetics MITOCW enzyme_kinetics In beer and wine production, enzymes in yeast aid the conversion of sugar into ethanol. Enzymes are used in cheese-making to degrade proteins in milk, changing their solubility,

More information

IVIVC Industry Perspective with Illustrative Examples

IVIVC Industry Perspective with Illustrative Examples IVIVC Industry Perspective with Illustrative Examples Presenter: Rong Li Pfizer Inc., Groton, CT rong.li@pfizer.com 86.686.944 IVIVC definition 1 Definition A predictive mathematical treatment describing

More information

Nonlinear Turnover Models for Systems with Physiological Limits

Nonlinear Turnover Models for Systems with Physiological Limits December 5, 8 Nonlinear Turnover Models for Systems with Physiological Limits Lambertus A. Peletier and Johan Gabrielsson Abstract Physiological limits have so far not played a central role in mechanism-based

More information

Synaptic dynamics. John D. Murray. Synaptic currents. Simple model of the synaptic gating variable. First-order kinetics

Synaptic dynamics. John D. Murray. Synaptic currents. Simple model of the synaptic gating variable. First-order kinetics Synaptic dynamics John D. Murray A dynamical model for synaptic gating variables is presented. We use this to study the saturation of synaptic gating at high firing rate. Shunting inhibition and the voltage

More information

Modelling a complex input process in a population pharmacokinetic analysis: example of mavoglurant oral absorption in healthy subjects

Modelling a complex input process in a population pharmacokinetic analysis: example of mavoglurant oral absorption in healthy subjects Modelling a complex input process in a population pharmacokinetic analysis: example of mavoglurant oral absorption in healthy subjects Thierry Wendling Manchester Pharmacy School Novartis Institutes for

More information

It can be derived from the Michaelis Menten equation as follows: invert and multiply with V max : Rearrange: Isolate v:

It can be derived from the Michaelis Menten equation as follows: invert and multiply with V max : Rearrange: Isolate v: Eadie Hofstee diagram In Enzymology, an Eadie Hofstee diagram (also Woolf Eadie Augustinsson Hofstee or Eadie Augustinsson plot) is a graphical representation of enzyme kinetics in which reaction velocity

More information

Estimating terminal half life by non-compartmental methods with some data below the limit of quantification

Estimating terminal half life by non-compartmental methods with some data below the limit of quantification Paper SP08 Estimating terminal half life by non-compartmental methods with some data below the limit of quantification Jochen Müller-Cohrs, CSL Behring, Marburg, Germany ABSTRACT In pharmacokinetic studies

More information

arxiv: v1 [q-bio.cb] 21 Dec 2015

arxiv: v1 [q-bio.cb] 21 Dec 2015 arxiv:1512.6896v1 [q-bio.cb] 21 Dec 215 A mathematical model of granulopoiesis incorporating the negative feedback dynamics and kinetics of G-CSF/neutrophil binding and internalisation M. Craig A.R. Humphries

More information

G-CSF treatment of chemotherapy induced. neutropenia - Online supplement

G-CSF treatment of chemotherapy induced. neutropenia - Online supplement G-CSF treatment of chemotherapy induced neutropenia - Online supplement Eliezer Shochat and Vered Rom-Kedar Weizmann Institute of Science May 31, 2008 1 The online supplement begins with introducing the

More information

PET Tracer Kinetic Modeling In Drug

PET Tracer Kinetic Modeling In Drug PET Tracer Kinetic Modeling In Drug Discovery Research Applications Sandra M. Sanabria-Bohórquez Imaging Merck & Co., Inc. Positron Emission Tomography - PET PET is an advanced d imaging i technique permitting

More information

MODELING THE ABSORPTION, CIRCULATION, AND METABOLISM OF TIRAPAZAMINE

MODELING THE ABSORPTION, CIRCULATION, AND METABOLISM OF TIRAPAZAMINE MODELING THE ABSORPTION, CIRCULATION, AND METABOLISM OF TIRAPAZAMINE Olivia Nguyen and Xiaoyu Shi Problem Statement: Tirapazamine (TPZ; 1,2,4-benzotriazin-3-amine 1,4-dioxide) is a hypoxia-activated prodrug

More information

Introduction to PK/PD modelling - with focus on PK and stochastic differential equations

Introduction to PK/PD modelling - with focus on PK and stochastic differential equations Downloaded from orbit.dtu.dk on: Feb 12, 2018 Introduction to PK/PD modelling - with focus on PK and stochastic differential equations Mortensen, Stig Bousgaard; Jónsdóttir, Anna Helga; Klim, Søren; Madsen,

More information

Supporting Information

Supporting Information Supporting Information For paper entitled: A Mechanistic Model of the Intravitreal Pharmacokinetics of Large Molecules and the Pharmacodynamic Suppression of Ocular VEGF Levels by Ranibizumab in Patients

More information

ENZYME KINETICS. Medical Biochemistry, Lecture 24

ENZYME KINETICS. Medical Biochemistry, Lecture 24 ENZYME KINETICS Medical Biochemistry, Lecture 24 Lecture 24, Outline Michaelis-Menten kinetics Interpretations and uses of the Michaelis- Menten equation Enzyme inhibitors: types and kinetics Enzyme Kinetics

More information

Hierarchical expectation propagation for Bayesian aggregation of average data

Hierarchical expectation propagation for Bayesian aggregation of average data Hierarchical expectation propagation for Bayesian aggregation of average data Andrew Gelman, Columbia University Sebastian Weber, Novartis also Bob Carpenter, Daniel Lee, Frédéric Bois, Aki Vehtari, and

More information

Satish Chandra. Unit I, REAL GASES. Lecture Notes Dated: Dec 08-14, Vander-Waals Gas

Satish Chandra. Unit I, REAL GASES. Lecture Notes Dated: Dec 08-14, Vander-Waals Gas Vander-Waals Gas Lecture Notes Dated: Dec 08-14, 01 Many equations have been proposed which describe the pvt relations of real gases more accurately than does the equation of state of an ideal gas. Some

More information

Evidence for the Existence of Non-monotonic Dose-response: Does it or Doesn t it?

Evidence for the Existence of Non-monotonic Dose-response: Does it or Doesn t it? Evidence for the Existence of Non-monotonic Dose-response: Does it or Doesn t it? Scott M. Belcher, PhD University of Cincinnati Department of Pharmacology and Cell Biophysics Evidence for the Existence

More information

Modelling the Dynamical State of the Projected Primary and Secondary Intra-Solution-Particle

Modelling the Dynamical State of the Projected Primary and Secondary Intra-Solution-Particle International Journal of Modern Nonlinear Theory and pplication 0-7 http://www.scirp.org/journal/ijmnta ISSN Online: 7-987 ISSN Print: 7-979 Modelling the Dynamical State of the Projected Primary and Secondary

More information

ENZYME SCIENCE AND ENGINEERING PROF. SUBHASH CHAND DEPARTMENT OF BIOCHEMICAL ENGINEERING AND BIOTECHNOLOGY IIT DELHI LECTURE 7

ENZYME SCIENCE AND ENGINEERING PROF. SUBHASH CHAND DEPARTMENT OF BIOCHEMICAL ENGINEERING AND BIOTECHNOLOGY IIT DELHI LECTURE 7 ENZYME SCIENCE AND ENGINEERING PROF. SUBHASH CHAND DEPARTMENT OF BIOCHEMICAL ENGINEERING AND BIOTECHNOLOGY IIT DELHI LECTURE 7 KINETICS OF ENZYME CATALYSED REACTIONS (CONTD.) So in the last lecture we

More information

PHAR 7632 Chapter 2 Background Mathematical Material

PHAR 7632 Chapter 2 Background Mathematical Material PHAR 7632 Chapter 2 Background Mathematical Material Student Objectives for this Chapter After completing the material in this chapter each student should:- understand exponents and logarithms, algebraically

More information

A primer on pharmacology pharmacodynamics

A primer on pharmacology pharmacodynamics A primer on pharmacology pharmacodynamics Drug binding & effect Universidade do Algarve Faro 2017 by Ferdi Engels, Ph.D. 1 Pharmacodynamics Relation with pharmacokinetics? dosage plasma concentration site

More information

Lecture # 3, 4 Selecting a Catalyst (Non-Kinetic Parameters), Review of Enzyme Kinetics, Selectivity, ph and Temperature Effects

Lecture # 3, 4 Selecting a Catalyst (Non-Kinetic Parameters), Review of Enzyme Kinetics, Selectivity, ph and Temperature Effects 1.492 - Integrated Chemical Engineering (ICE Topics: Biocatalysis MIT Chemical Engineering Department Instructor: Professor Kristala Prather Fall 24 Lecture # 3, 4 Selecting a Catalyst (Non-Kinetic Parameters,

More information

Discussion Exercise 5: Analyzing Graphical Data

Discussion Exercise 5: Analyzing Graphical Data Discussion Exercise 5: Analyzing Graphical Data Skill 1: Use axis labels to describe a phenomenon as a function of a variable Some value y may be described as a function of some variable x and used to

More information

CHAPTER 8 Analysis of FP Binding Data

CHAPTER 8 Analysis of FP Binding Data CHAPTER 8 Analysis of FP Binding Data Determination of Binding Constants............................................................8-2 Definitions.........................................................................8-2

More information

Supporting Information. Methods. Equations for four regimes

Supporting Information. Methods. Equations for four regimes Supporting Information A Methods All analytical expressions were obtained starting from quation 3, the tqssa approximation of the cycle, the derivation of which is discussed in Appendix C. The full mass

More information

Supplementary Figures

Supplementary Figures Supplementary Figures a x 1 2 1.5 1 a 1 = 1.5 a 1 = 1.0 0.5 a 1 = 1.0 b 0 0 20 40 60 80 100 120 140 160 2 t 1.5 x 2 1 0.5 a 1 = 1.0 a 1 = 1.5 a 1 = 1.0 0 0 20 40 60 80 100 120 140 160 t Supplementary Figure

More information

September Math Course: First Order Derivative

September Math Course: First Order Derivative September Math Course: First Order Derivative Arina Nikandrova Functions Function y = f (x), where x is either be a scalar or a vector of several variables (x,..., x n ), can be thought of as a rule which

More information

Understanding the Behavior of Systems Pharmacology Models Using Mathematical Analysis of Differential Equations: Prolactin Modeling as a Case Study

Understanding the Behavior of Systems Pharmacology Models Using Mathematical Analysis of Differential Equations: Prolactin Modeling as a Case Study Citation: CPT Pharmacometrics Syst. Pharmacol. (2016) 5, 339 351; VC 2016 ASCPT All rights reserved doi:10.1002/psp4.12098 TUTORIAL Models Using Mathematical Analysis of Differential Equations: Prolactin

More information

Compartmental Modelling: Eigenvalues, Traps and Nonlinear Models

Compartmental Modelling: Eigenvalues, Traps and Nonlinear Models Compartmental Modelling: Eigenvalues, Traps and Nonlinear Models Neil D. Evans neil.evans@warwick.ac.uk School of Engineering, University of Warwick Systems Pharmacology - Pharmacokinetics Vacation School,

More information

1 Periodic stimulations of the Incoherent Feedforward Loop network

1 Periodic stimulations of the Incoherent Feedforward Loop network 1 Periodic stimulations of the Incoherent Feedforward Loop network In this Additional file, we give more details about the mathematical analysis of the periodic activation of the IFFL network by a train

More information

Marsh Model. Propofol

Marsh Model. Propofol Marsh Model Propofol This work was supported by FEDER founds through COMPETE-Operational Programme Factors of Competitiveness ( Programa Operacional Factores de Competitividade") and by Portuguese founds

More information

A. One-Substrate Reactions (1) Kinetic concepts

A. One-Substrate Reactions (1) Kinetic concepts A. One-Substrate Reactions (1) Kinetic concepts (2) Kinetic analysis (a) Briggs-Haldane steady-state treatment (b) Michaelis constant (K m ) (c) Specificity constant (3) Graphical analysis (4) Practical

More information

Integration of SAS and NONMEM for Automation of Population Pharmacokinetic/Pharmacodynamic Modeling on UNIX systems

Integration of SAS and NONMEM for Automation of Population Pharmacokinetic/Pharmacodynamic Modeling on UNIX systems Integration of SAS and NONMEM for Automation of Population Pharmacokinetic/Pharmacodynamic Modeling on UNIX systems Alan J Xiao, Cognigen Corporation, Buffalo NY Jill B Fiedler-Kelly, Cognigen Corporation,

More information

APPLICATION OF LAPLACE TRANSFORMS TO A PHARMACOKINETIC OPEN TWO-COMPARTMENT BODY MODEL

APPLICATION OF LAPLACE TRANSFORMS TO A PHARMACOKINETIC OPEN TWO-COMPARTMENT BODY MODEL Acta Poloniae Pharmaceutica ñ Drug Research, Vol. 74 No. 5 pp. 1527ñ1531, 2017 ISSN 0001-6837 Polish Pharmaceutical Society APPLICATION OF LAPLACE TRANSFORMS TO A PHARMACOKINETIC OPEN TWO-COMPARTMENT BODY

More information

over K in Glial Cells of Bee Retina

over K in Glial Cells of Bee Retina Online Supplemental Material for J. Gen. Physiol. Vol. 116 No. 2 p. 125, Marcaggi and Coles A Cl Cotransporter Selective for 4 over K in Glial Cells of Bee Retina Païkan Marcaggi and Jonathan A. Coles

More information

Diffusion fronts in enzyme-catalysed reactions

Diffusion fronts in enzyme-catalysed reactions Diffusion fronts in enzyme-catalysed reactions G.P. Boswell and F.A. Davidson Division of Mathematics and Statistics, School of Technology University of Glamorgan, Pontypridd, CF37 DL, Wales, U.K. Department

More information

6-3 Solving Systems by Elimination

6-3 Solving Systems by Elimination Another method for solving systems of equations is elimination. Like substitution, the goal of elimination is to get one equation that has only one variable. To do this by elimination, you add the two

More information

On the status of the Michaelis-Menten equation and its implications for enzymology

On the status of the Michaelis-Menten equation and its implications for enzymology 1 On the status of the Michaelis-Menten equation and its implications for enzymology Sosale Chandrasekhar 1 Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India 1 E-mail:

More information

Computers, Lies and the Fishing Season

Computers, Lies and the Fishing Season 1/47 Computers, Lies and the Fishing Season Liz Arnold May 21, 23 Introduction Computers, lies and the fishing season takes a look at computer software programs. As mathematicians, we depend on computers

More information

COMPUTER AIDED DRUG DESIGN (CADD) AND DEVELOPMENT METHODS

COMPUTER AIDED DRUG DESIGN (CADD) AND DEVELOPMENT METHODS COMPUTER AIDED DRUG DESIGN (CADD) AND DEVELOPMENT METHODS DRUG DEVELOPMENT Drug development is a challenging path Today, the causes of many diseases (rheumatoid arthritis, cancer, mental diseases, etc.)

More information

Correction of the likelihood function as an alternative for imputing missing covariates. Wojciech Krzyzanski and An Vermeulen PAGE 2017 Budapest

Correction of the likelihood function as an alternative for imputing missing covariates. Wojciech Krzyzanski and An Vermeulen PAGE 2017 Budapest Correction of the likelihood function as an alternative for imputing missing covariates Wojciech Krzyzanski and An Vermeulen PAGE 2017 Budapest 1 Covariates in Population PKPD Analysis Covariates are defined

More information

Problem Set 5 Question 1

Problem Set 5 Question 1 2.32 Problem Set 5 Question As discussed in class, drug discovery often involves screening large libraries of small molecules to identify those that have favorable interactions with a certain druggable

More information

R7.3 Receptor Kinetics

R7.3 Receptor Kinetics Chapter 7 9/30/04 R7.3 Receptor Kinetics Professional Reference Shelf Just as enzymes are fundamental to life, so is the living cell s ability to receive and process signals from beyond the cell membrane.

More information

Robust design in model-based analysis of longitudinal clinical data

Robust design in model-based analysis of longitudinal clinical data Robust design in model-based analysis of longitudinal clinical data Giulia Lestini, Sebastian Ueckert, France Mentré IAME UMR 1137, INSERM, University Paris Diderot, France PODE, June 0 016 Context Optimal

More information

Biotransport: Principles

Biotransport: Principles Robert J. Roselli Kenneth R. Diller Biotransport: Principles and Applications 4 i Springer Contents Part I Fundamentals of How People Learn (HPL) 1 Introduction to HPL Methodology 3 1.1 Introduction 3

More information

Calcium dynamics, 7. Calcium pumps. Well mixed concentrations

Calcium dynamics, 7. Calcium pumps. Well mixed concentrations Calcium dynamics, 7 Calcium is an important ion in the biochemistry of cells Is used a signal carrier, i.e. causes contraction of muscle cells Is toxic at high levels The concentration is regulated through

More information

G. GENERAL ACID-BASE CATALYSIS

G. GENERAL ACID-BASE CATALYSIS G. GENERAL ACID-BASE CATALYSIS Towards a Better Chemical Mechanism via Catalysis There are two types of mechanisms we ll be discussing this semester. Kinetic mechanisms are concerned with rate constants

More information

Program for the rest of the course

Program for the rest of the course Program for the rest of the course 16.4 Enzyme kinetics 17.4 Metabolic Control Analysis 19.4. Exercise session 5 23.4. Metabolic Control Analysis, cont. 24.4 Recap 27.4 Exercise session 6 etabolic Modelling

More information

Basic Concepts in Population Modeling, Simulation, and Model-Based Drug Development Part 2: Introduction to Pharmacokinetic Modeling Methods

Basic Concepts in Population Modeling, Simulation, and Model-Based Drug Development Part 2: Introduction to Pharmacokinetic Modeling Methods Tutorial Citation: CPT: Pharmacometrics & Systems Pharmacology (3), e38; doi:.38/psp.3.4 3 ASCPT All rights reserved 63-836/ www.nature.com/psp Basic Concepts in Population Modeling, Simulation, and Model-Based

More information

10A. EVALUATION OF REACTION RATE FORMS IN STIRRED TANK. Most of the problems associated with evaluation and determination of proper rate forms from

10A. EVALUATION OF REACTION RATE FORMS IN STIRRED TANK. Most of the problems associated with evaluation and determination of proper rate forms from UPDATED 04/0/05 0A. EVALUATIO OF REACTIO RATE FORMS I STIRRED TAK REACTORS Most of the problems associated with evaluation and determination of proper rate forms from batch data are related to the difficulties

More information

Analysis of Allosterism in Functional Assays a

Analysis of Allosterism in Functional Assays a JPET This Fast article Forward. has not been Published copyedited and on formatted. July 26, The 2005 final as version DOI:10.1124/jpet.105.090886 may differ from this version. Analysis of Allosterism

More information

Chemical kinetics and catalysis

Chemical kinetics and catalysis Chemical kinetics and catalysis Outline Classification of chemical reactions Definition of chemical kinetics Rate of chemical reaction The law of chemical raction rate Collision theory of reactions, transition

More information

Chapter One. Introduction

Chapter One. Introduction Chapter One Introduction With the ever-increasing influence of mathematical modeling and engineering on biological, social, and medical sciences, it is not surprising that dynamical system theory has played

More information

Bioinformatics 3. V18 Kinetic Motifs. Fri, Jan 8, 2016

Bioinformatics 3. V18 Kinetic Motifs. Fri, Jan 8, 2016 Bioinformatics 3 V18 Kinetic Motifs Fri, Jan 8, 2016 Modelling of Signalling Pathways Curr. Op. Cell Biol. 15 (2003) 221 1) How do the magnitudes of signal output and signal duration depend on the kinetic

More information

Chemistry 112 Chemical Kinetics. Kinetics of Simple Enzymatic Reactions: The Case of Competitive Inhibition

Chemistry 112 Chemical Kinetics. Kinetics of Simple Enzymatic Reactions: The Case of Competitive Inhibition Chemistry Chemical Kinetics Kinetics of Simple Enzymatic Reactions: The Case of Competitive Inhibition Introduction: In the following, we will develop the equations describing the kinetics of a single

More information

How antibody surface coverage on nanoparticles determines the. activity and kinetics of antigen capturing for biosensing

How antibody surface coverage on nanoparticles determines the. activity and kinetics of antigen capturing for biosensing How antibody surface coverage on nanoparticles determines the activity and kinetics of antigen capturing for biosensing Bedabrata Saha, Toon H. Evers, and Menno W. J. Prins Philips Research, High Tech

More information

Bioinformatics 3! V20 Kinetic Motifs" Mon, Jan 13, 2014"

Bioinformatics 3! V20 Kinetic Motifs Mon, Jan 13, 2014 Bioinformatics 3! V20 Kinetic Motifs" Mon, Jan 13, 2014" Modelling of Signalling Pathways" Curr. Op. Cell Biol. 15 (2003) 221" 1) How do the magnitudes of signal output and signal duration depend on the

More information

Elementary reactions. stoichiometry = mechanism (Cl. + H 2 HCl + H. ) 2 NO 2 ; radioactive decay;

Elementary reactions. stoichiometry = mechanism (Cl. + H 2 HCl + H. ) 2 NO 2 ; radioactive decay; Elementary reactions 1/21 stoichiometry = mechanism (Cl. + H 2 HCl + H. ) monomolecular reactions (decay: N 2 O 4 some isomerisations) 2 NO 2 ; radioactive decay; bimolecular reactions (collision; most

More information

arxiv: v1 [q-bio.cb] 13 Jan 2017

arxiv: v1 [q-bio.cb] 13 Jan 2017 Predicting the dynamics of bacterial growth inhibition by ribosome-targeting antibiotics arxiv:1701.03702v1 [q-bio.cb] 13 Jan 2017 Philip Greulich, 1, 2 Jakub Doležal, 3 Matthew Scott, 4 Martin R. Evans,

More information

IDENTIFICATION OF PARAMETERS FOR HILL CURVE USED IN GENERAL ANESTHESIA

IDENTIFICATION OF PARAMETERS FOR HILL CURVE USED IN GENERAL ANESTHESIA IDENTIFICATION OF PARAMETERS FOR HILL CURVE USED IN GENERAL ANESTHESIA Diego F. Sendoya-Losada Department of Electronic Engineering, Faculty of Engineering, Surcolombiana University, Neiva, Huila, Colombia

More information

Sample Questions for the Chemistry of Life Topic Test

Sample Questions for the Chemistry of Life Topic Test Sample Questions for the Chemistry of Life Topic Test 1. Enzymes play a crucial role in biology by serving as biological catalysts, increasing the rates of biochemical reactions by decreasing their activation

More information

Enzymes Part III: Enzyme kinetics. Dr. Mamoun Ahram Summer semester,

Enzymes Part III: Enzyme kinetics. Dr. Mamoun Ahram Summer semester, Enzymes Part III: Enzyme kinetics Dr. Mamoun Ahram Summer semester, 2015-2016 Kinetics Kinetics is deals with the rates of chemical reactions. Chemical kinetics is the study of the rates of chemical reactions.

More information

Description of UseCase models in MDL

Description of UseCase models in MDL Description of UseCase models in MDL A set of UseCases (UCs) has been prepared to illustrate how different modelling features can be implemented in the Model Description Language or MDL. These UseCases

More information

Engineering Model Reduction and Entropy-based Lyapunov Functions in Chemical Reaction Kinetics

Engineering Model Reduction and Entropy-based Lyapunov Functions in Chemical Reaction Kinetics Entropy 2010, 12, 772-797; doi:10.3390/e12040772 Article OPEN ACCESS entropy ISSN 1099-4300 www.mdpi.com/journal/entropy Engineering Model Reduction and Entropy-based Lyapunov Functions in Chemical Reaction

More information

Mathematical Model of Catalytic Chemical Reactor. Sintayehu Agegnehu Matintu* School of Mathematical and Statistical Sciences, Hawassa University,

Mathematical Model of Catalytic Chemical Reactor. Sintayehu Agegnehu Matintu* School of Mathematical and Statistical Sciences, Hawassa University, Mathematical Model of Catalytic Chemical Reactor Sintayehu Agegnehu Matintu* School of Mathematical and Statistical Sciences, Hawassa University, P.O.Box 05, Hawassa, Ethiopia Abstract This study concerns

More information

II. An Application of Derivatives: Optimization

II. An Application of Derivatives: Optimization Anne Sibert Autumn 2013 II. An Application of Derivatives: Optimization In this section we consider an important application of derivatives: finding the minimum and maximum points. This has important applications

More information

2. Under what conditions can an enzyme assay be used to determine the relative amounts of an enzyme present?

2. Under what conditions can an enzyme assay be used to determine the relative amounts of an enzyme present? Chem 315 In class/homework problems 1. a) For a Michaelis-Menten reaction, k 1 = 7 x 10 7 M -1 sec -1, k -1 = 1 x 10 3 sec -1, k 2 = 2 x 10 4 sec -1. What are the values of K s and K M? K s = k -1 / k

More information

The Hurewicz Theorem

The Hurewicz Theorem The Hurewicz Theorem April 5, 011 1 Introduction The fundamental group and homology groups both give extremely useful information, particularly about path-connected spaces. Both can be considered as functors,

More information

Dr. Trent L. Silbaugh, Instructor Chemical Reaction Engineering Final Exam Study Guide

Dr. Trent L. Silbaugh, Instructor Chemical Reaction Engineering Final Exam Study Guide Chapter 1 Mole balances: Know the definitions of the rate of reaction, rate of disappearance and rate of appearance Know what a rate law is Be able to write a general mole balance and know what each term

More information

Lecture 4 STEADY STATE KINETICS

Lecture 4 STEADY STATE KINETICS Lecture 4 STEADY STATE KINETICS The equations of enzyme kinetics are the conceptual tools that allow us to interpret quantitative measures of enzyme activity. The object of this lecture is to thoroughly

More information

CHAPTER 4 Chemical Kinetics: Rate and Mechanistic Models. 4.1 Introduction

CHAPTER 4 Chemical Kinetics: Rate and Mechanistic Models. 4.1 Introduction CHAPE 4 Chemical Kinetics: ate and Mechanistic Models 4. Introduction By listing the plausible reaction stoichiometries, we can calculate the composition of the system in its final state, i.e. at equilibrium,

More information

Chemistry 112 Final Exam, Part II February 16, 2005

Chemistry 112 Final Exam, Part II February 16, 2005 Name KEY. (35 points) Consider the reaction A + B + C + D + E + F Æ P, which has a rate law of the following form: d[p]/dt = k[a]a[b]b[c]c[d]d[e]e[f]f The data sets given or displayed below were obtained

More information

Statistical mechanics of biological processes

Statistical mechanics of biological processes Statistical mechanics of biological processes 1 Modeling biological processes Describing biological processes requires models. If reaction occurs on timescales much faster than that of connected processes

More information

Stability Analysis and Numerical Solution for. the Fractional Order Biochemical Reaction Model

Stability Analysis and Numerical Solution for. the Fractional Order Biochemical Reaction Model Nonlinear Analysis and Differential Equations, Vol. 4, 16, no. 11, 51-53 HIKARI Ltd, www.m-hikari.com http://dx.doi.org/1.1988/nade.16.6531 Stability Analysis and Numerical Solution for the Fractional

More information